pipelines.chromake.scripts.paths

pipelines.chromake.scripts.paths

The paths module of chromake contains functions to identify the inputs and the files generated by the chromake pipeline.

Functions

Name Description
get_all_project_peaks Get the files necessary for the macs3 rules of all projects.
get_all_sequencings_related_paths Get the path to the files generated by the pipeline for the samples of all sequencings and projects.
get_project_paths_for_macs Get the files necessary for the macs2/macs3 rules of a project.
get_sequencings_related_paths Get the path to the files generated by the pipeline for the samples of a specific sequencing.

get_all_project_peaks

pipelines.chromake.scripts.paths.get_all_project_peaks(cfg)

Get the files necessary for the macs3 rules of all projects.

Parameters

Name Type Description Default
cfg dict Dict representing the configuration of an analysis with the chromake pipeline. required

Returns

Name Type Description
A list of files outputed by macs2 or macs3

get_project_paths_for_macs

pipelines.chromake.scripts.paths.get_project_paths_for_macs(
    cfg,
    project_name,
    mode,
)

Get the files necessary for the macs2/macs3 rules of a project.

Parameters

Name Type Description Default
cfg dict Dict representing the configuration of an analysis with the chromake pipeline. required
project_name str String representing the name of the project in cfg required
mode str String indicating the output. Accepted values are: - macs (dict with all inputs and the outputs of the macs3 command for all samples associated with the project) - macs_output (list of all outputs of the macs3 command for the project) required

Returns

Name Type Description
A dictionary of all file paths for the project.